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USCT data challenge

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SPIEDigitalLibrary.org/conference-proceedings-of-spie

USCT data challenge

Nicole V. Ruiter, Michael Zapf, Torsten Hopp, Hartmut

Gemmeke, Koen W. A. van Dongen

Nicole V. Ruiter, Michael Zapf, Torsten Hopp, Hartmut Gemmeke, Koen W.

A. van Dongen, "USCT data challenge," Proc. SPIE 10139, Medical Imaging
2017: Ultrasonic Imaging and Tomography, 101391N (13 March 2017); doi:
10.1117/12.2272593

Event: SPIE Medical Imaging, 2017, Orlando, Florida, United States

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 USCT data challenge
Nicole V. Ruiter1, Michael Zapf1, Torsten Hopp1, Hartmut Gemmeke1, Koen W.A. van Dongen2
1
Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Karlsruhe,
Germany
2
Laboratory of Acoustical Wavefield Imaging, Delft University of Technology, Delft, the
Netherlands

ABSTRACT
In the past years we have perceived within the USCT research community a demand for freely available USCT data sets.
Inspired by the idea of Open Science, this collection of data sets could stimulate the collaboration and the exchange of
ideas and experiences between USCT researchers. In addition, it may lead to comprehensive comparison of different
reconstruction algorithms and their results. Finally, by collecting feedback from the users about data and system
architecture, valuable information is gathered for further development of measurement setups. For the above reasons, we
have initiated a digital portal with several reference data sets and access scripts under free licenses. To kick off this
initiative, we organized a USCT data challenge event at SPIE Medical Imaging 2017.

Keywords: Ultrasound computer tomography, data challenge, open science, open data

1. INTRODUCTION

Ultrasound Computer Tomography is an exciting new technology mostly aimed at breast cancer imaging. Due to the
complex interaction of ultrasound with human tissue, the large amount of raw data, and the large volumes of interest,
image reconstruction is challenging both from a physical and a computational point of view. Many different image
reconstruction methods can be applied, ranging from simple ray based methods to full inversion with very different
approximations of the linear acoustic wave equation, see e.g. [1]. While the ray based algorithms offer fast
reconstruction, the inversion algorithms promise high image quality and resolution.

In recent years various groups have proposed a number of different approaches for image reconstruction, e.g. [1-23].
Direct comparison and analysis of the algorithms is difficult as they are usually applied to simulated data or – if available
– to real data acquired with very different measurement setups, e.g. [24-28]. The relatively few experimental data sets are
usually not commonly available. Moreover, even if they would be readily available, using the different date sets to test a
new reconstruction method would require accurate (and often not freely available) knowledge about the experimental
setup and data handling.

To mitigate such challenges for the scientific communities, there is an ongoing endeavor for so-called “Open science”.
Several leading European academic institutions signed in 2003 the “Berlin Declaration” on “open access to knowledge”
to enable easier exchange, participation and collaboration within the scientific community [33-35].

Following this idea and to mend gaps within the US(C)T community, the establishment of open and easy to use data and
code interfaces is the long term goal of this initiative. To stimulate the exchange of the available reconstruction
algorithms and raw data sets of different USCT devices, a reference database with freely available and open licensed
USCT data for comparison of reconstruction algorithms will be established, maintained and updated. Additionally, the
feedback about data and system architecture of the scientists working on reconstruction methods will help to drive
further development of the various measurement setups.

2. DESCRIPTION OF CHALLENGE
This challenge aims on applying available image reconstruction algorithms on provided USCT data in order to establish
a first intercommunication and standards for open data interface. In addition, this challenge marks the start of the USCT
reference database. The data sets and software for data access are available via the USCT challenge home page and the
linked data and code repository [29]. The long term goals of this work is to build up a free and open licensed reference

Medical Imaging 2017: Ultrasonic Imaging and Tomography, edited by Neb Duric, Brecht Heyde, Proc. of
SPIE Vol. 10139, 101391N · © 2017 SPIE · CCC code: 1605-7422/17/$18 · doi: 10.1117/12.2272593

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 ! .,_----__.,^-

Figure 1: The two

t scanning syystems; (left) sketch of the US
SCT system fro
om the TU Delfft: a water tankk with a rotating g object (tissue
mimicking agaar phantom of approx.
a 20 mm x 50 mm) emullating a rotatingg source at a raddial distance off 0.3 m and a ro
otating receiver
at a radial disttance of 0.1 m; (right) KIT 3D3 USCT: USC CT with patien
nt bed (center), transducer apeerture (top righ ht) and patient
position (bottom right).

USCT data base

b which iss available forr the whole community.
c We
W expect thiis to enable rreproducible comparison
c of
image reconsstruction algorrithms and USSCT systems and to establish user frienddly and easy to use interfaaces, standardss
and data form
mats between the
t different USCT
U systemss and their recconstruction allgorithms, sofftware and datta formats.

The materialss are providedd using a free and open liceense, i.e. the BSDB 3-clause license [30] ffor code and data, allowingg
free use and publication
p off results. Afterr the challengee the data setss may remain with
w the particcipants, and can
c be used forr
additional ressearch and othher purposes. Further publiication and reesults should follow
f good aacademic pracctices and citee
this paper.

The participaants are encouuraged to a submit field reeport to the SPIE

S Medicall image confeerence 2017. This report iss
preferably baased on the prrovided field report templaate and may contain
c mation about the applied algorithm
inform a (e.gg.
citation of paaper), and – if available – reconstructedd images and performance results. The pparticipants ag gree that theirr
participation and their resuults may be published
p in connection
c wiith their namees and affiliattions, also und der a free andd
open license and open acceess standards. The participaants are also invited
i to sharre their resultss, feedback an
nd suggestionss
at the poster session
s and thhe open panel discussion of the SPIE Ultrrasonic Imaginng and Tomoggraphy conferrence.

3. USC
CT SYSTEM OF
O TU DELF
FT
The Delft Brreast Ultrasouund Scanner (DBUS) is deppicted on the left-hand sidde of Figure 11. The system m consists of a
water tank with
w dimensionns 0.75 m x 0.75 0 m x 0.655 m with a waater level of 0.45 0 m. The ttemperature ofo the water iss
continuously monitored viaa thermocouples and kept constant
c n 1oC using heating
within h mats annd a temperatture controllerr.
On top of thee system, two rotary stages (LG Motion LGR1090-PD D), controlled by motor drivvers (Parker),, are mountedd.
The first rotaary stage rotaates the objectt, the second the receiver (0.5 MHz, Paanametrics V3318). The sou urce, which iss
identical to thhe receiver, is mounted at a fixed positionn in the cornerr of the tank. In
I this way a 22D tomograph hic scan of thee
object is obtaained. For eacch A-scan, ann electric pulsse with a centter frequency of approx. 00.5 MHz is geenerated by ann
arbitrary wavve form generrator (Agilent 33250A), am mplified (Electtronics and Innnovation 2100L 40 dB), and d successivelyy
damped usingg a variable atttenuator (JFW W Industries, 50BR-036).
5 The
T resulting wavew field is m
measured usin
ng an identicaal
transducer coonnected to a 14 bit A/D converter (S Spectrum M3i.4142-exp - PCI) which is set to a sample rate of
400 MHz. Foor each A-scaan, in additionn to the raw (unfiltered)
( R data, information such as temperaturre, source andd
RF
receiver posittions, etc. is stored.
s Togethher with a scann including ann object, a scaan in absence of an object, referred to ass
an empty scann, is made forr reference. An
A example off an empty scaan is shown inn Figure 2. Thhe A-scan, preesented in timee
and frequencyy domain, corrresponds to a measurementt with the sourrce and receivver facing eachh other.

4. USCT
U SYSTE
EM OF KIT
The KIT’s 3DD Ultrasound Computer Toomography sysstem (3D USC CT) is depicteed on the rightt hand side off Figure 1. Thee
device has a semi-ellipsoiddal 3D apertuure. Approx. sppherical wavee fronts are geenerated by eaach emitter att 2.5 MHz andd

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 20 Iog10[ IP0,0)1 / maxt0í10,0)1) ]
o

-10
0.2
-20
Ñ n4
E -30
.- 0.6
-40

0.8
-50

-60
50 100 150 200 250 300 350
[o]

5 -40

1 ô -50
ó
co
0.5 -60
ii
ii 0 o.
-70

-0.5 -80
o
1 ti -90

-1.5 -100
0.25 0.3 0.35 0 0.2 0.4 0.6 0.8 1

t [ms] f [MHz]

Figure 2: The RF data measured with the DBUS system in absence of an object; (top) B-scan showing the field measured as a
function of time and receiver angle for single source position; (bottom-left and -right) single A-scan in time and frequency domain.

with a bandwidth of 1.5 MHz at -6 dB. The semi-elliptical aperture has a diameter of 26 cm and a height of 16 cm.
Rotational and translational movements, so-called aperture positions, of the complete sensor system create additional
virtual positions of the transducers.

The 2041 individual transducers are either operated as emitter (628) or receiver (1413). The transducers have opening
angles of 38.2° (standard deviation ±1.5°) at -6 dB. Four emitters and nine receivers are grouped together including pre-
amplifier and control electronics in so-called Transducer Array Systems (TAS). Each of the 157 TAS contains a
temperature sensor for tracking the temperature distribution within the water basin and the shift at each TAS position
during measurements. Additionally, two calibrated PT100 temperature sensors are embedded in the TAS holder to
enable increased accuracy.

The data acquisition is carried out with an FPGA based system, which can store up to 80 of A-scans [31]. The
digitalization is performed by 480 parallel channels (12 at 20 ), enabling data acquisition at one aperture
position in approx. ten seconds. After digitization, the parallel data streams are processed as follows: First, the data
streams are bandpass filtered (1.67 to 3.33 at −60 ). Next, the data rate is reduced by a factor of six by
performing bandpass undersampling. Finally, the reduced data is stored in the internal memory buffer. Using this
approach up to 47 data sets at different aperture positions can be stored in one data acquisition step. A detailed
description of the 3D USCT system can be found in [32].

The emitters are excited with a coded excitation signal, e.g. frequency coded chirps can be applied to increase the signal-
to-noise ratio of the data. Also the gain of the receiving channels is set individually based on an initial measurement. The
applied coded excitation, the individual gain, the temperature data and the spatial positions of the aperture are stored along
with the A-scans for each measurement and can be used for signal (pre-) processing and image reconstruction. Empty
measurements are also provided and exemplary data is depicted in Figure 3.

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 -4 |p(t,n )|
x 10 tas
0

0.5

time/s
1.5

2.5

20 40 60 80 100 120 140

n
tas
5
x 10 1

0.8
1
0.6

0.4
0.5
0.2

Amplitude
p(t)

0 0

-0.2

-0.5 -0.4

-0.6
-1
-0.8

1.4 1.6 1.8 2 2.2 2.4 -1

0 0.5 1 1.5 2 2.5 3
t/s -4
x 10 time in seconds -5
10

Figure 3: RF data measured with the 3D USCT system in absence of an object; (top) B-scan of the raw data of one emitter in the first
TAS of top transducer row of aperture as a function of time and one receiver of each TAS counter-clockwise from top to bottom;
bottom-left shows a single A-scan (receiver opposite of emitter element) in time and bottom-right a frequency coded chirp applied
for coded excitation.

5. DATASETS
In total eight data sets have been made available; two sets are obtained with the system from the TU Delft, and six with
the system from KIT. The data is available under “Open Data Commons Attribution License” and the access scripts
under the 3-clause BSD license.

A compact overview of the available data sets is presented in Table 1 and Figure 4 shows photos of the phantoms and
exemplary reconstructed slices.

TU Delft data sets

Two data sets are provided by the TU Delft. The first data set is made in absence of an object and can be used as
reference measurement. It covers one source and 450 receiver positions equally distributed over 360o. The second data
set is an agar based phantom with dimensions of 20 mm x 50 mm, and covers 45 source and 450 receiver positions, all
equally distributed over 360o. The tissue mimicking phantom has a volume density of mass of approx. 1004 kg/m3 and a
speed of sound of approx. 1479 m/s. However, care has to be taken with these values as the conditions under which these
values have been obtained may deviate from the actual scanning conditions. The three inclusions were generated by
embedding drinking straws in the agar based phantom during curing. Prior to scanning the object, the straws were
removed and the inclusions were filled with water.

KIT data set

Three data sets of different phantoms are provided, each with an empty scan acquired at the same day as the phantom
and identical settings of the system’s parameters.

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 TU Delft aggar based phanttom KIIT gelatin 3

KIT turkey phantom K

KIT nylon threaad phantom

Figure 4: Phanntoms scanned; (left) photo, (rright) reconstruuction using different reconstrruction algorithhms. From top left to bottom
right: TU Delfft: agar based phantom
p reconsstructed with Delay
D and Sum;; KIT: gelatin 3 phantom recoonstructed with h SAFT in low
resolution and displayed as maximum
m intenssity projection to
t enhance the visibility of the bottom of thee plastic cup, tu
urkey phantom
reconstructed with
w SAFT, andd finally nylon thread
t phantomm with speed of sound correctedd SAFT reconstruction.

Gelatin 3: Thhe phantom coonsists of a geelatin phantomm with diameeter of approx. 0.07 m at thhe bottom and d 0.10 m at thee
top, a height of approx. 0.113 m of whichh approx. 0.100 m where immmersed into thhe USCT aperrture. The speeed of sound of
the gelatin was
w approx. 15151 m/s. Thee gelatin wass embedded in i a plastic cup.
c Two inclusions were generated byy
embedding drrinking strawss with diameteer 5 mm in thee gelatin durin
ng curing. Prioor to scanningg the object, th
he straws weree
removed andd the inclusionns were filledd with water. The phantom m was positiooned approx. centrally in the 3D USCT T
aperture.

Turkey phanttom: Two olivves without sttones where embedded

e intto a turkey steeak. This steaak was then embedded
e in a
condom and filled with geelatin. The reesulting phanttom has a diaameter of apprrox. 9 cm. Thhe phantom was w positionedd
approx. centrrally in the 3D
D USCT apertture. The turkkey steak had an approximaate sound speeed of > 1550 m/s while thee
olives had a sound
s speed of approx. 1450 m/s.

Nylon threadds: The phanttom consists of

o a gelatin cylinder
c with both diameteer and heightt of approx. 10
1 cm. In thiss
cylinder a nyylon thread of
o diameter 0.2
0 mm is em mbedded. The phantom waas centrally positioned in thet 3D USCT T
aperture.

6. FUTURE
E PROSPECTIIVE FOR USC
CT REFERE
ENCE DATA BASE

The aim of thhis work is to start a freely available USC CT data base enabling to teest and analyzze reconstructiion algorithmss
or to comparre the perform mance of com mpeting algorithms. In a first step inittial data basee entries are provided andd
participants of
o this challennge are asked tot report theirr experiences in using the data.
d Additionnally a panel discussion
d willl

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 allow discussing the first steps towards standardized interfaces to access the data of very different USCT systems and
brainstorming about specifications for phantoms and real patient data to be included in the data base.

Table 1: Overview of the scans made available.

TU Delft KIT
Object None (empty scan) None (empty scan) with parameters
fitting gelatin 3 measurement
Center frequency / bandwidth / 0.5 MHz / - / - 2.5 MHz / 2.67 MHz / 25.6 µs
chirp length
Original sampling rate (stored) 400 MHz (400 MHz) 20 MHz (6.6 MHz)
NAperture pos. x NSource x NReceiver 1 x 1 x 450 10 x (157 x 4) x (157 x 9)
TU Delft KIT
Object Agar based tissue mimicking phantom Gelatin phantom with two water
inclusions (Gelatin 3)
Center frequency / bandwidth / 0.5 MHz / - / - 2.5 MHz / 2.67 MHz / 25.6 µs
chirp length
Original sampling rate (stored) 400 MHz (400 MHz) 20 MHz (6.6 MHz)
NAperture pos. x NSource x NReceiver 1 x 45 x 450 10 x (157 x 4) x (157 x 9)
KIT KIT
Object None (empty scan) with parameters None (empty scan) with parameters
fitting Turkey phantom measurement fitting Nylon threads measurement
Center frequency / bandwidth / 2.5 MHz / 2.67 MHz / 25.6 µs 2.5 MHz / 2.67 MHz / 25.6 µs
chirp length
Original sampling rate (stored) 20 MHz (6.6 MHz) 20 MHz (6.6 MHz)
NAperture pos. x NSource x NReceiver 20 x (157 x 4) x (157 x 9) 1 x (157 x 4) x (157 x 9)
KIT KIT
Object Turkey phantom: Olives embedded in Nylon thread embedded in gelatin
a turkey steak and gelatin cylinder
Center frequency / bandwidth / 2.5 MHz / 2.67 MHz / 25.6 µs 2.5 MHz / 2.67 MHz / 25.6 µs
chirp length
Original sampling rate (stored) 20 MHz (6.6 MHz) 20 MHz (6.6 MHz)
NAperture pos. x NSource x NReceiver 20x (157 x 4) x (157 x 9) 23 x (157 x 4) x (157 x 9)

After the kick off of opening the data base for the public and establishing easy to use data access further challenges are
planned, e.g. challenging the different algorithms by comparison of obtained image quality or computational
performance. The data sets are freely available and open licensed, so they can also be used outside of challenges for
evaluation of advanced reconstruction techniques on real data, further development of algorithms for image
reconstruction and signal processing.

The feedback about data and USCT systems resulting from the use with different algorithms can also lead to drive
further development of the system architecture, e.g. to research the optimization of transducer positioning or limits on
signal-to-noise levels.

We hope also that these challenges will lead to a growth of the data base by increasing the number of imaged objects
and/or data acquired with different USCT architectures.

Finally, the overall motivation for all of our work is to support early breast cancer diagnosis. Thus, we also need to learn
more about the properties of breast cancer tissues and how to image them to make the most distinguishing properties
available for diagnosis. This upcoming knowledge needs to be included into the data base by imaging and if possible
quantify the properties of appropriate phantoms and tissue structures.

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 ACKNOWLEDGEMENT

The authors would like to acknowledge the following people: Bastiaan Dekker and Elmer Jansen for building the 2D
setup and performing the measurements; Clemens Kaiser, Wei Yap Tan and Carina Wittenbeck for building and
measuring phantoms for the 3D USCT and the many colleagues in the institutes who made the built up of USCT systems
possible.

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[30] https://opensource.org/licenses/BSD-3-Clause
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Proc. of SPIE Vol. 10139 101391N-8

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